On 10/5/19 11:11 AM, Quin K wrote:
To see if complex is stable and to see how it fluctuate in the binding
site.
Stability of the complex can mean multiple things. If you want to show
that the protein structure is stable in the presence of the ligand, you
would compute the RMSD of the protein (probably backbone) and compare
the result against that of an apo simulation. If you want to show that
the complex is stable in terms of the association of the protein and
ligand, that's not something you do via RMSD; you compute distances,
angles, etc. related to the interactions of the protein that hold the
ligand in the active site.
You need to define what "it" is in the context of fluctuations.
Fluctuation of the ligand in the binding can be computed by calculating
RMSD of the ligand after a fit to the protein (to get relative motion).
You can also do RMSF (e.g. of binding site residues, again to be
compared against apo data for context/control).
-Justin
On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 10/5/19 10:53 AM, Quin K wrote:
Hi,
*What should I pick for RMSD analysis of protein ligand complex? *
*What other analysis can be done for protein ligand complex? *
Following are the options I have for least square fit and for RMSD
calculation.
MPPA is the ligand I used.
Group 0 ( System) has 50085 elements
Group 1 ( Protein) has 4590 elements
Group 2 ( Protein-H) has 2307 elements
Group 3 ( C-alpha) has 282 elements
Group 4 ( Backbone) has 846 elements
Group 5 ( MainChain) has 1127 elements
Group 6 ( MainChain+Cb) has 1396 elements
Group 7 ( MainChain+H) has 1399 elements
Group 8 ( SideChain) has 3191 elements
Group 9 ( SideChain-H) has 1180 elements
Group 10 ( Prot-Masses) has 4590 elements
Group 11 ( non-Protein) has 45495 elements
Group 12 ( Other) has 31 elements
Group 13 ( MPPA) has 31 elements
Group 14 ( NA) has 2 elements
Group 15 ( Water) has 45462 elements
Group 16 ( SOL) has 45462 elements
Group 17 ( non-Water) has 4623 elements
Group 18 ( Ion) has 2 elements
Group 19 ( MPPA) has 31 elements
Group 20 ( NA) has 2 elements
Group 21 ( Water_and_ions) has 45464 elements
Group 22 ( Protein_MPPA) has 4621 elements
Thanks & regards!
What is your objective in calculating RMSD?
-Justin
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Justin A. Lemkul, Ph.D.
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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